Learn to use Molecular Modeling Database, or MMDB , which is Entrez's structural database brought to you by the National Institutes of Health and the National Center for Biotechnology Information. It contains an extensive collection of three-dimensional structures with detailed annotation that can be used to learn about the structure and function of many proteins. MMDB's structures were originally obtained from PBD and they contain descriptions, references and extensive multi-directional links both inside and outside of the NCBI network. There are pre-computed structural homologs, i.e. related structures or neighbors, that you can access, and extensive visualization and comparative analysis tools that you can use to examine individual structures, or multiple structures aligned.

You will learn:

  • to search MMDB using both basic and advanced query techniques
  • how to understand the detailed results you obtain
  • methods to visualize and manipulate structures using NCBIs Cn3D structural viewer
  • to locate and view structurally aligned homologs


This tutorial is a part of the tutorial group Protein-centric and protein structure resources. You might find the other tutorials in the group interesting:

Pfam: Protein Domain families

UniProt: UniProt, Universal Protein Resource

RCSB PDB: RCSB Protein Data Bank

Entrez Protein: NCBI's Entrez Protein for amino acid-centric information

Structural Biology Knowledgebase: The Protein Structure Initiative Structural Biology Knowledgebase


Proteins : Tools that are primarily used in the storage, retrieval, or exploration of amino acid based data. Some tools may also involve nucleotide sequence information.

NCBI : This category includes resources maintained at the National Center for Biotechnology Information (NCBI).


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Gardner G Stewart et al., Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli Selected articles from The 11th Annual Biotechnology and Bioinformatics Symposium (BIOT-2014): Genetics The 11th Annual Biotechnology and Bioinformatics Symposium (BIOT-2014). BMC Genetics (2015) doi:10.1186/1471-2156-16-S2-S2

Kelley A Lawrence et al., Partial protein domains: evolutionary insights and bioinformatics challenges. Genome Biology (2015) doi:10.1186/s13059-015-0663-8